Mitton:
It's kind of amusing that you're asking what the BIG questions in
MICRObiology are. Welcome to the biggest little field. We're glad
you've come over from physics to a living science...
The way I see it, as a microbial ecologist, the biggest questions to be
asked in microbiology are pertaining to the ecology of microbes. We have
only been able to isolate and grow an estimated 0.1-1% of ALL bacteria
thought to exists. But beyond merely studying them in the lab, we need
to more about how these little critters survive in the environment, even
in SOLID ROCK several hundred meters below the surface (look up papers by
P. Amy). It's mind boggling!!! And to top it off, we are still only in
the very early stages of understanding how microbes interact in
populations, communities and with other trophic levels in a wide variety
of environements.
I'd say any area of general microbial ecology will lead you into the BIG
questions that need to be answered.
Sincerely,
Mark E. Fuller